I'm working on the next update for my blog, which will have additional pictures of the various steps, but here's the process:
Build up the topography with latex modeling putty.
Prime.
After painting the model in question, give the entire base a heavy coat of thinned Gorthor Brown.
Cover the "water" areas with a heavy coat of Stirland Mud (straight from the pot), building up a bank between these areas and the "dry land" areas.
Give the "dry land" areas a heavy coat of thinned wood glue, add substrate. I'm currently using a mix of Army Painter's Brown Battlefield and a cheaper generic equivalent I had laying around.
Give the substrate a second heavy coat of thinned wood glue to seal it. Patch any areas where the substrate has come loose.
Wash the "dry land" areas twice with Agrax Earthshade, avoiding the mud.
For rocks: Paint with two coats of Dawnstone, wash with Nuln Oil.
Seal the bank with 'Ardcoat - I haven't tested this yet, but it should alleviate some of the issues I'm seeing with the water effect. Yeah, definitely don't do this.
Add the water effect. I'm currently using Vallejo's Still Water, best applied in multiple coats with 12 hours of set time in between.
Clean up any cracks/bubbles in the water effect with heavy applications of 'Ardcoat.
For pond scum: Wash along the banks with Agrax Earthshade.
For muddy water: Wash desired areas with Agrax Earthshade, then seal with 'Ardcoat.
Add flora. I'm currently using Army Painter's Swamp Tufts (green) and Highland Tufts (brown). The bushes are lichen sealed with thinned-down wood glue. Once mounted, wash the perimeter with Agrax Earthshade to blend them to the base and hide any stray glue.
Add moss. This is simply a liberal application of Lustrian Undergrowth.
Paint the rim of the base black (or your preferred color).
Consume whiskey.